Last week, I texted the comedian Josie Long to tell her I was writing an article about why there are so few women standups, and to ask for her opinion. This was her reply: "Do you know how often I get asked this question? It's killing me! Every five minutes the same question and [in] interviews! It's a real pet peeve because it makes me feel like I almost shouldn't be doing what I do."

Long's irritation with the question is good-natured (every female standup I speak to feels something similar), but it's not a subject that's going away any time soon. I've asked it ceaselessly while preparing a list of great standup performances for a new Guardian online series: so far I've got to 95 men and 16 women. Can this be right? Or evidence of my own latent sexism?

There is an opinion at large out there, which Long estimates she hears 300 times a year: that women aren't funny. Or, the deluxe version: that women are only funny rarely, and certainly less often than men. Some evolved genetic disadvantage (the details of which we'll gloss over) is apparently holding women back. A bold theory, is perhaps the politest thing to call that.

So what is the problem? Lara A King, recent winner of the Funny Women award, does not believe that men are funnier. "Just because there are more men doing it, that doesn't necessarily mean they are better at it. I think they get given the breaks a bit more, and they get given a little bit more slack. I think women are less encouraged and less supported. People who book comedy nights do tend to think that one woman on the bill is really quite enough."

This last point is widely made. "Bookers will spread you out," says Sarah Millican, "maybe because there's only about 10 or 12 [women] at [a particular] level. A bit like they might spread out the one-liner guys. You're kind of a bracket on your own – which is fine. I understand that people want variety on a bill. It's also positive discrimination in a way. They might like to have a woman on the bill."

Is this really fine? Are women comics so similar they can be treated as a genre? Female standups surely vary as much as male ones. Millican often performs routines about her relationship with food, for instance, but insists that roughly half her audience are men. "Yes, I'm coming from a viewpoint, because that's the only viewpoint I have," she says. "But if you're funny, they laugh."

Limiting women standups to one per bill might be part of the picture, but that picture might not look very different if women were distributed randomly. Chortle, the industry website, reports that around 20% of the entries for its student comedy award come from women, and its own large but imperfect catalogue of working comedians lists 239 women and 1,130 men – suggesting that one woman to every four men is a roughly fair reflection of the people who become standups.

It also suggests a problem that starts early. And when women see so few other women on the circuit, and on awards lists, this is hardly a surprise. The Funny Women awards were created with the hope of changing this; other awards are meant to be blind to anything but quality. Half the judges who produced Chortle's almost all-male 2012 shortlist were women, explains the website's editor, Steve Bennett. "It doesn't, admittedly, look great," he says. "But what should we have done about it?"

What indeed? Isy Suttie is an established standup (you might remember her as Dobby in Peep Show) and is firmly against positive discrimination, whether from judges or promoters. "I don't feel we get patronised like that, thankfully," she says. "I sometimes feel I get booked because I've been on TV, more than because I'm a woman." But then Suttie doesn't feel she receives much negative discrimination, either. "To me, it isn't a big problem," she says. "There are loads of female standups. I'm sure it's changed. I think in the 1980s and 1990s it was much harder for women. We should be grateful to Jo Brand, Jenny Eclair et al for paving the way for us."

I have no doubt Suttie is sincere, but it is easy to see why some would be reluctant to grumble about the industry. Laughter is to comedians what money is to bankers: you either make it or you don't, and only the unfunny need excuses. The unarguable success of Millican offers hope. Her most recent DVD sold 241,000 copies in 2011, which is a lot. Her first TV series, The Sarah Millican Television Programme, recently launched on BBC2 and is getting good ratings (and it is funny). But this is very much a career and not a crusade she has embarked on. "I am genuinely a comic before I am a woman," she says. "It sounds ridiculous, but I have never felt more at home than I do on stage. Ever."

BBC comedy controller Cheryl Taylor recalls a mostly male audience at a recent Millican gig in Halifax – including "60- or 70-year-old Yorkshiremen all cracking up and falling around". So wWhat about women on the BBC? In January, the corporation was criticised in a report which found a lack of women on comedy programmes such as QI and Mock the Week, shows that mostly book guests from the standup circuit. (Outside panel shows, the picture is more even.) "In my world, and in my day-to-day conversations and meetings, I never really feel that it's in any sense dominated by men," Taylor says. "I'm aware that if you tot things up numerically, there are more male comedians around than female comedians, and probably more male comedy writers, but it doesn't strike me that it's a crisis."

Television, of course, has always recruited women for sitcoms and sketch shows, and French and Saunders, Mrs Merton, the Royle Family, Nighty Night and others have been proving women's funniness for years. In their variety, they also prove that there is no such thing as "women's comedy". And there are signs that stage performers are beginning to escape the designation, too. (I defy anyone to see a female connection between the work of Suttie, Walsh, Long and Conti.) Khorsandi's act is more or less unconcerned with her gender, and she is thriving. US comic Sarah Silverman is interested in taboos, not gender, and is one of American standup's biggest stars.

Is it too hopeful to imagine that this generation of successful women is encouraging another, bigger wave? I ask Millican if Jo Brand inspired her. "Absolutely!" comes the answer. "She's our queen! I can't imagine what it must have been like for her to stand up on stage when she was such a rarity. But I am so grateful that she did, because it has made my life so much easier, and it's definitely paved the way for us. And in turn, we are paving the way for the next lot. Who's to say, maybe at some point in the not too distant future, there'll be no paving that needs to be done. It will be entirely paved. We will have a lovely patio of female comics." That sounds like something worth crusading for.

• Leo Benedictus's comedy gold, a series on the world's greatest standups, starts today with Sarah Silverman at theguardian.com/comedy

• This article was amended on 21 March 2012. The original named Dana Alexander as Dana Hall. This has been corrected.